If your baby has a strong heartbeat he is likely fine. You just aren't as far along as you thought.
If it's night, use a dusk, and if asleep use Aultra ball or heal. If you want to take a good risk use a poke ball. All 3 are really great at catching Rakou. I even caught Red Gyarados, Moltrace and Entei with one.
He is how you do so, I know because I used my master ball on kyoger but still caught latias. First you need, (this also is the exact same for latios) -Latias in your pokedex -a Pokemon with mean look or block (preflebly wobefet) have them holding quick claw -20 NEST balls, and 10 ultra balls - a Pokemon with sweet scent (could use trousous (the frut Pokemon) ) First look in your pokedex to see where she is. (if she is not in your pokedex you have to get lucky by trawling through the hoenn). Once you know where she is travel there ON FOOT, not using fly, and not using a bike. Once you are where you need to be, use sweet scent. There is an 85.7% chance if your in the right area that Latias will attack you. When she does use block or mean look first and it will Not work if the Pokemon is not holdin quick claw.Once it says that Latias cannot escape attack it with wak attacks until it is in red. Because nest balls work best on weak Pokemon, just keep on throwing them first. If you run out throw ulrta balls. As soon as you caught it voila! You have Latias!!